write_grange_to_vcf: Write a GRange to a vcf file

In popopo19/excerno: Fillter out somatic mutations generated by the Formalin-Fixed Paraffin-Embedded (FFPE) tissue preservation technique from cancer tissue

Write a GRange to a vcf file

Description

Write a GRange to a vcf file

Usage

write_grange_to_vcf(grange, file.name)

Arguments

grange	A grange object with columns id, ref, alt, qual, filter, info
file.name	A string of the new file name. Make sure to end string with ".vcf"

Examples

library(MutationalPatterns)
library(tidyverse)
library(Biostrings)
library(BSgenome.Hsapiens.UCSC.hg38)
library(vcfR)

set.seed(10)

# Load in signatures
cosmic.sigs <- get_known_signatures()
cosmic.sig4 <- as.matrix(cosmic.sigs[,4])
ffpe.sig <- get_ffpe_signature()

# Create samples
sample.sig4 <- create_signature_sample_vector(cosmic.sig4, 100)
sample.ffpe <- create_signature_sample_vector(ffpe.sig, 100)

# Create classification data frame
samples <- list(sample.sig4, sample.ffpe)
signatures <- list(cosmic.sig4, ffpe.sig)
classify.df <- classify_simulated_samples(samples, signatures)

seq <- getSeq(Hsapiens, "chr1")

set.seed(10)
info <- sample("SOMATIC", 200, replace = TRUE)
quality <- sample(50:100, 200, replace = TRUE)
filter <- sample("PASS", 200, replace = TRUE)
format <- sample("GT:GQ", 200, replace = TRUE)
samples <- list(sample(paste("0/0:", 1:100, sep = ""), 200, replace = TRUE), sample(paste("0/0:", 1:100, sep = ""), 200, replace = TRUE))
sample.names <- c("SAMPLE1", "SAMPLE2")
set.seed(10)
classify.gr <- create_gr_from_sample(classify.df, seq, "chr1", info, quality, filter, format, samples, sample.names)

# Funtion usage
file.name <- "new_file.vcf"
write_grange_to_vcf(classify.gr, file.name)

popopo19/excerno documentation built on Aug. 28, 2022, 1:23 a.m.